BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524287.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,916,732 number of mapped reads = 1,770,755 (92.38%) number of supplementary alignments = 6,394 (0.33%) number of secondary alignments = 0 number of mapped bases = 103,647,463 bp number of sequenced bases = 103,616,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,110 duplication rate = 3.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2971 >>>>>>> ACTG content number of A's = 25,983,912 bp (25.08%) number of C's = 18,350,742 bp (17.71%) number of T's = 32,522,752 bp (31.39%) number of G's = 26,745,393 bp (25.81%) number of N's = 13,339 bp (0.01%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 510,874 number of insertions = 6,072 mapped reads with insertion percentage = 0.34% number of deletions = 19,450 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.9% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.3399X There is a 2.96% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8327488 0.03341009930723503 0.7057712351234086 chr2 243199373 8748264 0.03597157300236954 0.350580973254158 chr3 198022430 6777405 0.03422544102705941 0.20333161251390489 chr4 191154276 6739587 0.03525731749783091 0.23750214908158235 chr5 180915260 6310028 0.034878362389109685 0.20768779025965295 chr6 171115067 5850731 0.03419179329193729 0.2231733672332316 chr7 159138663 5675934 0.03566659347892096 0.45073185380242925 chr8 146364022 5463971 0.03733138052191542 0.34299180506426447 chr9 141213431 4360291 0.030877310813303586 0.2898357384597004 chr10 135534747 5031183 0.03712098271006475 0.316011355426473 chr11 135006516 4767879 0.03531591764059744 0.28985494335945394 chr12 133851895 4592299 0.03430880825407814 0.21142942977073625 chr13 115169878 3247377 0.028196409133992482 0.18453281585191958 chr14 107349540 3151961 0.02936166284457297 0.2017853842197865 chr15 102531392 2922905 0.028507415563030686 0.18503869701247483 chr16 90354753 3042014 0.03366744857351334 0.21908672198212195 chr17 81195210 2757830 0.03396542727089443 0.22292999219690382 chr18 78077248 2840974 0.03638670768723816 0.5811638686346949 chr19 59128983 2078334 0.03514915857761328 0.4487372271523475 chr20 63025520 2198826 0.034887867644725505 0.21019179059394985 chr21 48129895 1370868 0.028482671736557913 0.21494686816823538 chr22 51304566 1230760 0.023989287815045546 0.17000874074597885 chrMT 16571 6943 0.4189849737493211 0.7196470936281735 chrX 155270560 5818164 0.037471134257517975 0.24661694307055315 chrY 59373566 335447 0.005649770135079979 0.1626343120682448